Zinc in PDB 3psq: Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis

The structure of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis, PDB code: 3psq was solved by H.J.Kang, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.32
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.511, 94.511, 253.519, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 26.2

The structure of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis (pdb code 3psq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 19 binding sites of Zinc where determined in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis, PDB code: 3psq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn314 b:74.8 occ:1.00 NE2 A:HIS149 2.1 54.8 1.0 O A:HOH303 2.1 52.2 1.0 O A:HOH244 2.5 59.9 1.0 CE1 A:HIS149 2.5 53.7 1.0 O A:HOH267 2.6 65.2 1.0 NZ A:LYS148 3.3 71.6 1.0 CD2 A:HIS149 3.4 52.7 1.0 ND1 A:HIS149 3.8 55.2 1.0 CD A:LYS148 4.1 69.0 1.0 CE A:LYS148 4.2 71.3 1.0 CG A:HIS149 4.2 55.7 1.0 CA A:GLY75 4.4 47.5 1.0 CE1 A:PHE145 4.5 48.9 1.0 O A:GLY75 4.8 47.6 1.0 CD1 A:PHE145 4.8 49.5 1.0 CG A:LYS148 5.0 63.3 1.0

Zinc binding site 2 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn316 b:33.5 occ:0.80 OD1 A:ASP223 2.0 56.4 1.0 ND1 A:HIS127 2.0 41.9 1.0 SG A:CYS221 2.3 44.6 1.0 O A:HOH280 2.3 42.0 1.0 CG A:ASP223 2.8 60.4 1.0 OD2 A:ASP223 2.9 59.9 1.0 CE1 A:HIS127 3.0 41.7 1.0 CG A:HIS127 3.1 39.0 1.0 CB A:CYS221 3.1 46.2 1.0 CB A:HIS127 3.4 40.3 1.0 CA A:HIS127 3.8 39.4 1.0 ND2 A:ASN131 3.9 42.1 1.0 NE2 A:HIS127 4.1 41.2 1.0 CD2 A:HIS127 4.2 38.0 1.0 CB A:ASP223 4.2 60.2 1.0 O A:HOH256 4.2 42.5 1.0 O A:HOH281 4.4 53.6 1.0 O A:HIS127 4.5 40.1 1.0 CA A:CYS221 4.6 47.0 1.0 C A:HIS127 4.6 39.7 1.0 CH3 A:ACY243 4.7 37.8 1.0 N A:ASP223 4.7 59.0 1.0 CA A:ASP223 4.8 60.9 1.0 C A:CYS221 4.9 48.8 1.0 N A:HIS127 5.0 40.2 1.0

Zinc binding site 3 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn317 b:82.9 occ:0.80 OE2 A:GLU237 2.0 73.8 1.0 O A:HOH292 2.2 72.3 1.0 O A:HOH304 2.4 70.3 1.0 OE1 A:GLU237 2.5 72.0 1.0 CD A:GLU237 2.6 70.8 1.0 O A:HOH291 3.4 60.4 1.0 CG A:GLU237 4.1 66.3 1.0 ND2 A:ASN165 4.2 49.6 1.0 OD1 A:ASN165 4.4 56.9 1.0 NZ A:LYS163 4.6 69.0 1.0 CG A:ASN165 4.7 52.3 1.0 CE A:LYS163 4.9 67.3 1.0 CB A:GLU237 5.0 63.9 1.0

Zinc binding site 4 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn320 b:86.6 occ:1.00 OE2 A:GLU155 2.2 61.6 1.0 O A:HOH289 2.3 67.1 1.0 O A:HOH247 2.9 74.7 1.0 CD A:GLU155 3.0 56.1 1.0 OE1 A:GLU155 3.2 59.5 1.0 CD A:LYS159 4.0 58.6 1.0 CE A:LYS161 4.2 71.8 1.0 NZ A:LYS53 4.3 76.4 1.0 NZ A:LYS161 4.3 75.2 1.0 CE A:LYS53 4.4 73.9 1.0 CG A:LYS159 4.5 58.6 1.0 CG A:GLU155 4.5 51.7 1.0 CB A:LYS159 4.7 57.6 1.0 CD A:LYS53 4.8 72.3 1.0 CE A:LYS159 4.9 58.5 1.0 NZ A:LYS159 4.9 58.4 1.0

Zinc binding site 5 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn324 b:71.2 occ:1.00 ND1 A:HIS196 1.9 58.0 1.0 CE1 A:HIS196 2.8 57.2 1.0 CG A:HIS196 3.0 56.7 1.0 CB A:HIS196 3.5 57.0 1.0 CA A:HIS196 4.0 56.2 1.0 NE2 A:HIS196 4.0 55.0 1.0 CD2 A:HIS196 4.1 55.7 1.0 OE2 A:GLU192 4.5 67.8 1.0 OG A:SER177 4.7 51.4 1.0 CD A:GLU192 4.7 69.9 1.0 OE1 A:GLU192 4.8 71.2 1.0 N A:HIS196 4.9 56.1 1.0

Zinc binding site 6 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn326 b:40.2 occ:1.00 OE2 A:GLU90 2.0 41.7 1.0 OD2 A:ASP66 2.0 46.6 1.0 O A:HOH268 2.0 38.1 1.0 OE2 A:GLU86 2.1 45.0 1.0 OE1 A:GLU86 2.6 44.9 1.0 CD A:GLU86 2.7 45.6 1.0 CD A:GLU90 2.8 43.8 1.0 CG A:ASP66 2.9 43.7 1.0 OE1 A:GLU90 2.9 44.9 1.0 OD1 A:ASP66 3.0 42.2 1.0 NZ A:LYS94 3.8 46.8 1.0 OH A:TYR91 4.1 40.2 1.0 CG A:GLU86 4.2 44.8 1.0 CG A:GLU90 4.2 42.6 1.0 N A:GLU86 4.3 43.1 1.0 CB A:ASP66 4.3 44.1 1.0 O A:HOH258 4.3 50.2 1.0 CA A:GLY85 4.3 42.6 1.0 O A:HOH290 4.4 53.8 1.0 CE2 A:TYR91 4.4 39.3 1.0 CZ A:TYR91 4.7 41.3 1.0 O A:GLN84 4.7 40.7 1.0 C A:GLY85 4.7 42.9 1.0

Zinc binding site 7 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn329 b:51.8 occ:1.00 O A:HOH254 1.8 47.0 1.0 O A:HOH262 2.0 47.1 1.0 O A:HOH258 2.1 50.2 1.0 O A:HOH266 2.2 40.5 1.0 O A:HOH263 2.4 58.4 1.0 O A:HOH288 4.1 59.6 1.0 OE1 A:GLN84 4.1 38.2 1.0 O A:HOH246 4.2 56.8 1.0 OD1 A:ASP66 4.2 42.2 1.0 O A:GLN84 4.2 40.7 1.0 OE2 A:GLU86 4.3 45.0 1.0 O A:GLY85 4.9 43.9 1.0 CG A:GLU86 4.9 44.8 1.0

Zinc binding site 8 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn330 b:38.2 occ:1.00 OXT A:ACY243 1.9 38.9 1.0 ND1 A:HIS126 1.9 39.6 1.0 C A:ACY243 2.7 39.5 1.0 CE1 A:HIS126 2.8 39.1 1.0 O A:ACY243 2.9 38.6 1.0 CG A:HIS126 3.0 40.6 1.0 CB A:HIS126 3.5 39.5 1.0 NE2 A:HIS126 3.9 36.4 1.0 CD2 A:HIS126 4.1 39.5 1.0 CA A:HIS126 4.1 39.5 1.0 CH3 A:ACY243 4.2 37.8 1.0 O A:HOH318 4.2 52.2 1.0 N A:HIS127 4.4 40.2 1.0 CD1 A:ILE92 4.7 39.1 1.0 CG1 A:ILE92 4.8 40.3 1.0 C A:HIS126 4.9 40.0 1.0

Zinc binding site 9 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn312 b:56.9 occ:1.00 O B:HOH264 2.1 48.3 1.0 O B:HOH255 2.2 58.7 1.0 O B:HOH265 2.3 55.5 1.0 O B:HOH27 2.4 49.3 1.0 O B:HOH261 2.5 59.2 1.0 O B:HOH248 2.8 44.9 1.0 O B:HOH284 3.7 54.4 1.0 O B:GLN84 4.1 44.0 1.0 O B:HOH286 4.1 47.5 1.0 OE1 B:GLN84 4.3 47.5 1.0 OD1 B:ASP66 4.3 42.5 1.0 OE2 B:GLU86 4.6 40.0 1.0 CG B:GLU86 4.7 39.3 1.0 O B:GLY85 4.7 45.4 1.0 C B:GLY85 4.9 43.8 1.0 C B:GLN84 4.9 44.2 1.0

Zinc binding site 10 out of 19 in the Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn313 b:76.7 occ:0.80 OE2 B:GLU136 2.1 62.1 1.0 ND1 B:HIS77 2.2 56.0 1.0 CE1 B:HIS77 2.6 55.8 1.0 CD B:GLU136 3.1 55.4 1.0 OE1 B:GLU136 3.5 56.2 1.0 CG B:HIS77 3.6 52.4 1.0 ND2 B:ASN131 3.6 51.6 0.5 CG B:ASN131 3.7 52.1 0.5 NE2 B:HIS77 3.9 57.6 1.0 OD1 B:ASN131 4.0 53.2 0.5 N B:HIS77 4.2 49.1 1.0 O B:HOH303 4.2 57.1 1.0 ND2 B:ASN131 4.2 52.8 0.5 CB B:ASN131 4.3 52.0 0.5 CB B:HIS77 4.3 49.5 1.0 CB B:ASN131 4.3 52.0 0.5 CG B:GLU136 4.3 48.1 1.0 CD2 B:HIS77 4.4 53.7 1.0 C B:THR76 4.7 50.0 1.0 O B:HOH304 4.7 57.9 1.0 CG B:ASN131 4.8 52.4 0.5 CA B:HIS77 4.8 48.9 1.0 CA B:THR76 4.9 50.4 1.0

H.J.Kang, F.Coulibaly, T.Proft, E.N.Baker. Crystal Structure of SPY0129, A Streptococcus Pyogenes Class B Sortase Involved in Pilus Assembly Plos One V. 6 15969 2011.
ISSN: ESSN 1932-6203
PubMed: 21264317
DOI: 10.1371/JOURNAL.PONE.0015969